SMTL ID : 6sc6.1

dAb3/HOIP-RBR apo structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-2-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.3, C.6, C.26, C.29 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.3, A:C.6, A:C.26, A:C.29 ZN.2: 4 residues within 4Å: Chain A: C.21, C.23, C.48, C.51 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.21, A:C.23, A:C.48, A:C.51 ZN.3: 4 residues within 4Å: Chain A: C.103, C.106, C.121, C.124 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.103, A:C.106, A:C.121, A:C.124 ZN.4: 4 residues within 4Å: Chain A: C.129, C.132, H.140, C.145 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.129, A:C.132, A:H.140, A:C.145 ZN.5: 4 residues within 4Å: Chain A: C.175, C.178, C.194, C.197 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.175, A:C.178, A:C.194, A:C.197 ZN.6: 5 residues within 4Å: Chain A: C.202, C.205, H.230, C.234, F.236 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.202, A:C.205, A:H.230, A:C.234 ZN.7: 4 residues within 4Å: Chain A: C.215, C.220, H.227, H.229 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.215, A:C.220, A:H.227, A:H.229 ZN.8: 4 residues within 4Å: Chain A: C.273, C.290, C.302, H.305 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.273, A:C.290, A:C.302, A:H.305

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 5 residues within 4Å: Chain A: N.207, P.231, L.367, G.368, Q.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.207, A:Q.369 Water bridges: A:H.230, A:S.370 SO4.10: 5 residues within 4Å: Chain A: G.188, C.189, M.190, F.236, R.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.190, A:H.191 Salt bridges: A:R.239 SO4.11: 1 residues within 4Å: Chain A: R.336 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.336 SO4.14: 7 residues within 4Å: Chain A: Q.105 Chain B: S.52, P.53, I.54, G.55, T.56, Y.57 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:Q.135 Hydrogen bonds: B:S.52, B:S.52, B:I.54, B:G.55, B:T.56, B:T.56 SO4.15: 3 residues within 4Å: Chain B: F.27, T.28, Y.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:T.28, B:T.28, B:Y.32

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain A: L.101, W.102, K.133 Chain B: G.104 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain A: G.204, D.233, C.234, L.235, V.311, N.315 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, Y.I. et al., Single-Domain Antibodies as Crystallization Chaperones to Enable Structure-Based Inhibitor Development for RBR E3 Ubiquitin Ligases. Cell Chem Biol (2020)

Release Date

2019-11-27

Peptides

E3 ubiquitin-protein ligase RNF31: A
Single domain antibody: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E3 ubiquitin-protein ligase RNF31

Single domain antibody

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